1
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Cole F, Pfeiffer M, Wang D, Schröder T, Ke Y, Tinnefeld P. Controlled mechanochemical coupling of anti-junctions in DNA origami arrays. Nat Commun 2024; 15:7894. [PMID: 39256353 PMCID: PMC11387415 DOI: 10.1038/s41467-024-51721-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which-upon binding of trigger DNA strands-undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.
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Affiliation(s)
- Fiona Cole
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, Germany
- Center for NanoScience, Ludwig-Maximilians-Universität München, Schellingstraße 4, München, Germany
| | - Martina Pfeiffer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, Germany
- Center for NanoScience, Ludwig-Maximilians-Universität München, Schellingstraße 4, München, Germany
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
- Georgia Institute of Technology, Atlanta, GA, USA
- School of Biomedical Engineering, University of Science and Technology of China, Suzhou, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China
| | - Tim Schröder
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, Germany
- Center for NanoScience, Ludwig-Maximilians-Universität München, Schellingstraße 4, München, Germany
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA.
- Georgia Institute of Technology, Atlanta, GA, USA.
| | - Philip Tinnefeld
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, Germany.
- Center for NanoScience, Ludwig-Maximilians-Universität München, Schellingstraße 4, München, Germany.
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2
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Paul I, Valiyev I, Ghosh A, Schmittel M. Dynamic negative allosteric effect: regulation of catalysis via multicomponent rotor speed. Chem Commun (Camb) 2024; 60:7085-7088. [PMID: 38896476 DOI: 10.1039/d4cc02144d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Nanorotor R1 (420 kHz) was assembled from five components utilizing three orthogonal interactions. Post-modification at the distal position generated the advanced six component rotor R2 (45 kHz). The decrease in R2 speed leads to the inhibition of a three-component reaction by reducing catalyst release.
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Affiliation(s)
- Indrajit Paul
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany.
| | - Isa Valiyev
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany.
| | - Amit Ghosh
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany.
| | - Michael Schmittel
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie I, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany.
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3
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Mizuno H, Nakazawa H, Miyagawa A, Yakiyama Y, Sakurai H, Fukuhara G. Amplification sensing manipulated by a sumanene-based supramolecular polymer as a dynamic allosteric effector. Sci Rep 2024; 14:12534. [PMID: 38822045 PMCID: PMC11143208 DOI: 10.1038/s41598-024-63304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024] Open
Abstract
The synthesis of signal-amplifying chemosensors induced by various triggers is a major challenge for multidisciplinary sciences. In this study, a signal-amplification system that was flexibly manipulated by a dynamic allosteric effector (trigger) was developed. Herein, the focus was on using the behavior of supramolecular polymerization to control the degree of polymerization by changing the concentration of a functional monomer. It was assumed that this control was facilitated by a gradually changing/dynamic allosteric effector. A curved-π buckybowl sumanene and a sumanene-based chemosensor (SC) were employed as the allosteric effector and the molecular binder, respectively. The hetero-supramolecular polymer, (SC·(sumanene)n), facilitated the manipulation of the degree of signal-amplification; this was accomplished by changing the sumanene monomer concentration, which resulted in up to a 62.5-fold amplification of a steroid. The current results and the concept proposed herein provide an alternate method to conventional chemosensors and signal-amplification systems.
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Affiliation(s)
- Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8551, Japan
| | - Hironobu Nakazawa
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yumi Yakiyama
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
- Division of Applied Chemistry, Graduate School of Engineering and Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hidehiro Sakurai
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Division of Applied Chemistry, Graduate School of Engineering and Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8551, Japan.
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4
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Kundu S, Mondal D, Elramadi E, Valiyev I, Schmittel M. Parallel Allosteric Inhibition of Shuttling Motion and Catalysis in a Silver(I)-loaded [2]Rotaxane. Org Lett 2022; 24:6609-6613. [PMID: 36053156 DOI: 10.1021/acs.orglett.2c02609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A dynamic silver(I)-loaded [2]rotaxane shuttle (k298 = 135 kHz) was converted allosterically into a conformationally restricted [2]rotaxane due to the creation of a bulky imine in the center of the axle component. Only the dynamic silver(I)-loaded [2]rotaxane was able to catalyze a 6-endo-cyclization reaction, whereas the static one was catalytically quiet. The mechanism of catalyst deactivation was elucidated.
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Affiliation(s)
- Sohom Kundu
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Debabrata Mondal
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Emad Elramadi
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Isa Valiyev
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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5
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Suzuki S, Homma A, Nishi R, Mizuno H, Kawauchi S, Fukuhara G. A Dynamically Responsive Chemosensor That Can be Modulated by an Effector: Amplification Sensing by Positive Heterotropic Allosterism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sho Suzuki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Amane Homma
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Reiya Nishi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Susumu Kawauchi
- Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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6
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.
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Affiliation(s)
- Sarah E. Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843 USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Moscow Region, Russia 142290
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7
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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8
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9
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A dual-channel optical chemical sensing system for selective detection of nerve agent simulant DFP. Anal Bioanal Chem 2021; 413:4501-4509. [PMID: 34041577 DOI: 10.1007/s00216-021-03413-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
This paper reports a novel optical chemical sensing system for selective detection of diisopropylfluorophosphate (DFP), a simulant of fluorine-containing nerve agents (Sarin and Soman). Contrary to the reported methods involving only single sensing probe, this sensing system is comprised of two molecular sensing probes (1 and 2) having intrinsic affinities for reactive subunits of DFP (electrophilic phosphorus and fluoride ion). On exposure to DFP, two molecular probes react in tandem with electrophilic phosphorus and fluoride ion (by-product of the initial phosphorylation reaction) to induce a unique modulation in the optical properties of the sensing system which leads to selective detection of DFP in solution as interferents like phosphorus-containing compounds, acids, and anions were unable to induce similar optical modulation due to lack of both electrophilic phosphorus and fluorine in the same molecule. Calibration curve between the amount of DFP added and the absorption intensity revealed the colorimetric detection limit of the system to be 4.50 μM which was further lowered to 2.22 μM by making use of a self-immolative fluoride sensing probe 5.
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10
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Zhang Y, Zhang Q, Cheng F, Chang Y, Liu M, Li Y. Fast-responding functional DNA superstructures for stimuli-triggered protein release. Chem Sci 2021; 12:8282-8287. [PMID: 34221310 PMCID: PMC8221054 DOI: 10.1039/d1sc00795e] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/26/2022] Open
Abstract
Strategies that speed up the on-command release of proteins (e.g., enzymes) from stimuli-responsive materials are intrinsically necessary for biosensing applications, such as point-of-care testing, as they will achieve fast readouts with catalytic signal-amplification. However, current systems are challenging to work with because they usually exhibit response times on the order of hours up to days. Herein, we report on the first effort to construct a fast-responding gating system using protein-encapsulating functional DNA superstructures (denoted as protein@3D DNA). Proteins were directly embedded into 3D DNA during the one-pot rolling circle amplification process. We found that the specific DNA-DNA interaction and aptamer-ligand interaction could act as general protocols to release the loaded proteins from 3D DNA. The resulting gating system exhibits fast release kinetics on the order of minutes. Taking advantage of this finding, we designed a simple paper device by employing protein@3D DNA for colorimetric detection of toxin B (Clostridium difficile marker). This device is capable of detecting 0.1 nM toxin B within 16 minutes.
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Affiliation(s)
- Yuxin Zhang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology Dalian 116024 China
| | - Fang Cheng
- School of Chemical Engineering, Dalian University of Technology Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
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11
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Nan Y, Gu Y, Zhou Q, Zhao W, Zhang J. Ultra-low background signaling cascade amplifiers for in vivo fluorescence imaging of hydroxyl radical production induced by testosterone. NEW J CHEM 2021. [DOI: 10.1039/d1nj02772g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel ultra-low background signal cascade amplifier was developed to understand the production mechanism of ˙OH pools in situ stimulated by testosterone.
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Affiliation(s)
- Yanxia Nan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yu Gu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Qiulan Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Wenjie Zhao
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, China
| | - Jun Zhang
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, China
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12
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Hoffrichter G, Lützen A. Allosteric binding of sodium deoxycholate by a bis(β-cyclodextrin)-2,2′-bipyridine receptor. Org Chem Front 2021. [DOI: 10.1039/d1qo01173a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The allosteric effect of a new bis(β-cyclodextrin) receptor amounts to a more than 18-fold increase of its binding affinity towards sodium deoxycholate upon addition of a zinc(ii) phenanthroline complex as an effector.
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Affiliation(s)
- Gabriel Hoffrichter
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Arne Lützen
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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13
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Kang S, Park BY, Lee S, Lee N, Han MS. Colorimetric discrimination of nucleoside phosphates based on catalytic signal amplification strategy and its application to related enzyme assays. Analyst 2020; 146:463-470. [PMID: 33491016 DOI: 10.1039/d0an01918f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selective detection of adenosine monophosphate (AMP) and adenosine diphosphate (ADP) which are less charged molecules than adenosine triphosphate (ATP) or pyrophosphate (PPi) in aqueous solution has been considered challenging because AMP and ADP have relatively low binding affinity for phosphate receptors. In this study, colorimetric discrimination of nucleoside phosphates was achieved based on catalytic signal amplification through the activation of artificial peroxidase. This method showed high selectivity for AMP and ADP over ATP and PPi, unlike previous phosphate sensors that use Zn2+-dipicolylamine-based receptors. High selectivity of the suggested method allowed discrimination of AMP in aqueous solution by the naked eye, and the detection limit was estimated to be 0.5 μM. Mechanism analysis revealed AMP acted as activators in the peroxidation cycle of the Mn2(bpmp)/ABTS/H2O2 system despite having relatively low binding affinity. Additionally, high selectivity and quantitative signal amplification allowed for the development of colorimetric phosphodiesterase and a small molecule kinase assay method. The newly proposed method offers direct, real-time, and quantitative analysis of enzyme activities and inhibition, and is expected to be further applied to high-throughput screening of inhibitors.
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Affiliation(s)
- Seungyoon Kang
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.
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14
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Tsuchiya T, Fukuhara G. Allosteric Signal Amplification Sensing Using a Bisthiourea-Binaphthyl-Polythiophene Conjugate: A Positive Homotropic Allosterim Case. J Org Chem 2020; 85:13239-13245. [PMID: 32880172 DOI: 10.1021/acs.joc.0c01326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of signal amplification systems has attracted much attention and presents a highly challenging objective. Herein, we reveal the amplification processes using a newly synthesized bisthiourea-binaphthyl-polythiophene conjugate. The spectral data, behavior of supramolecular complexation, and thermodynamic parameters with calculation support comprehensively elucidated the factors that control the outcomes of the signal amplification. The present work provides a new perspective on functional chemosensors and an attractive alternative to conventional amplification systems.
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Affiliation(s)
- Tomoaki Tsuchiya
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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15
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An amplification-free method for the detection of HOTAIR long non-coding RNA. Anal Chim Acta 2020; 1132:66-73. [DOI: 10.1016/j.aca.2020.07.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/06/2023]
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16
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Biswas PK, Saha S, Gaikwad S, Schmittel M. Reversible Multicomponent AND Gate Triggered by Stoichiometric Chemical Pulses Commands the Self-Assembly and Actuation of Catalytic Machinery. J Am Chem Soc 2020; 142:7889-7897. [DOI: 10.1021/jacs.0c01315] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pronay Kumar Biswas
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Suchismita Saha
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Sudhakar Gaikwad
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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17
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Chen YH, Chien WC, Lee DC, Tan KT. Signal Amplification and Detection of Small Molecules via the Activation of Streptavidin and Biotin Recognition. Anal Chem 2019; 91:12461-12467. [DOI: 10.1021/acs.analchem.9b03144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Kui-Thong Tan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan (ROC)
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18
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19
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Ali M, Tsai TH, Braun PV. Amplified Detection of Chemical Warfare Agents Using Two-Dimensional Chemical Potential Gradients. ACS OMEGA 2018; 3:14665-14670. [PMID: 30555985 PMCID: PMC6289487 DOI: 10.1021/acsomega.8b01519] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Chemical warfare agents such as sarin are highly toxic, and detection of even trace levels is important. Using a hydrogel film containing a built-in two-dimensional chemical potential gradient, we demonstrate the detection of a sarin simulant under conditions potentially as low as a level 1 (6.90 × 10-9 mg/cm3 for 10 min) Acute Exposure Guideline Level sarin exposure. Specifically, the sarin simulant diisopropyl fluorophosphate (DFP) is aerosol-deposited on a hydrogel film containing a built-in ionic chemical gradient and the enzyme, diisopropyl fluorophosphatase (DFPase). DFPase degrades the DFP, releasing fluoride ions. The fluoride ions are then concentrated by the gradient to a miniature electrochemical sensor embedded in the hydrogel providing a 30-fold amplification of the fluoride ion signal, which is an indication of exposure to DFP, relative to a gradient-free system. This method is general for agents which hydrolyze into chemically detectable ionic species.
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20
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Sun X, Shabat D, Phillips ST, Anslyn EV. Self-Propagating Amplification Reactions for Molecular Detection and Signal Amplification: Advantages, Pitfalls, and Challenges. J PHYS ORG CHEM 2018; 31:e3827. [PMID: 30386006 PMCID: PMC6205521 DOI: 10.1002/poc.3827] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/11/2018] [Indexed: 01/09/2023]
Abstract
Self-propagating cascade reactions are a recent development for chemo-sensing protocols. These cascade reactions, in principle, offer low limits of detection by virtue of exponential signal amplification, and are initiated by a specific, pre-planned molecular detection event. This combination of selectivity for a detection event followed by in situ signal amplification is achieved by exploitation of mechanistic organic chemistry, and thus has resulted in various chemo-sensing protocols that employ one or more reagents to achieve the desired selectivity and sensitivity for an assay. Species such as hydrogen peroxide, thiols, and fluoride, have been used as active reagents to initiate the first examples of self-propagating signal amplification reactions, although many other active reagents should be compatible with the approaches. A common feature of the reagents that support the self-propagating signal amplification reactions is the involvement of quinonemethide intermediates resulting from elimination of optical reporters and/or active reagents, where the latter propagates the signal amplification reaction. The early examples of these amplification sequences, however, are slow to reach full signal, thus leaving time for background reactions to generate non-specific signals. This issue of background has limited practical applications of these self-propagating signal amplification reactions, as has challenging synthetic routes to the reagents, as well as the potential for other chemical species to interfere with the detection and signal amplification processes. Thus, the goal of this review is to summarize the progress of self-propagating signal amplification technology, identify the pitfalls of current designs, and by doing so, to stimulate future studies in this growing and promising research area.
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Affiliation(s)
- Xiaolong Sun
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, United States
| | - Doron Shabat
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Scott T Phillips
- Micron School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, United States
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21
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Teanphonkrang S, Janke S, Chaiyen P, Sucharitakul J, Suginta W, Khunkaewla P, Schuhmann W, Ruff A, Schulte A. Tuned Amperometric Detection of Reduced β-Nicotinamide Adenine Dinucleotide by Allosteric Modulation of the Reductase Component of the p-Hydroxyphenylacetate Hydroxylase Immobilized within a Redox Polymer. Anal Chem 2018; 90:5703-5711. [PMID: 29633834 DOI: 10.1021/acs.analchem.7b05467] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the fabrication of an amperometric NADH biosensor system that employs an allosterically modulated bacterial reductase in an adapted osmium(III)-complex-modified redox polymer film for analyte quantification. Chains of complexed Os(III) centers along matrix polymer strings make electrical connection between the immobilized redox protein and a graphite electrode disc, transducing enzymatic oxidation of NADH into a biosensor current. Sustainable anodic signaling required (1) a redox polymer with a formal potential that matched the redox switch of the embedded reductase and avoided interfering redox interactions and (2) formation of a cross-linked enzyme/polymer film for stable biocatalyst entrapment. The activity of the chosen reductase is enhanced upon binding of an effector, i.e. p-hydroxy-phenylacetic acid ( p-HPA), allowing the acceleration of the substrate conversion rate on the sensor surface by in situ addition or preincubation with p-HPA. Acceleration of NADH oxidation amplified the response of the biosensor, with a 1.5-fold increase in the sensitivity of analyte detection, compared to operation without the allosteric modulator. Repetitive quantitative testing of solutions of known NADH concentration verified the performance in terms of reliability and analyte recovery. We herewith established the use of allosteric enzyme modulation and redox polymer-based enzyme electrode wiring for substrate biosensing, a concept that may be applicable to other allosteric enzymes.
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Affiliation(s)
- Somjai Teanphonkrang
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Salome Janke
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry , Chulalongkorn University , 10330 Bangkok , Thailand
| | - Wipa Suginta
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand.,Center of Excellence (CoE) in Advanced Functional Materials, Institute of Science , Suranaree University of Technology , Nakhon Ratchasima 30000 , Thailand
| | - Panida Khunkaewla
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Wolfgang Schuhmann
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Adrian Ruff
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
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22
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Xiong S, Huang C. Synergistic strategies of predominant toxins in snake venoms. Toxicol Lett 2018; 287:142-154. [PMID: 29428543 DOI: 10.1016/j.toxlet.2018.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/17/2018] [Accepted: 02/03/2018] [Indexed: 12/22/2022]
Abstract
Synergism is a significant phenomenon present in snake venoms that may be an evolving strategy to potentiate toxicities. Synergism exists between different toxins or toxin complexes in various snake venoms, with phospholipaseA2s (PLA2s) (toxins or subunits) the main enablers. The predominant toxins, snake venom PLA2s, metalloproteases (SVMPs), serine proteases (SVSPs) and three-finger toxins (3FTxs), play essential roles in synergistic processes. The hypothetical mechanisms of synergistic effect can be generalized under the effects of amplification and chaperoning. The Toxicity Score is among the few quantitative methods to assess synergism. Selection of toxins involved in synergistically enhanced toxicity as the targets are important for development of novel antivenoms or inhibitors.
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Affiliation(s)
- Shengwei Xiong
- College of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, China
| | - Chunhong Huang
- College of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, China.
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23
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Pezzato C, Chen JLY, Galzerano P, Salvi M, Prins LJ. Catalytic signal amplification for the discrimination of ATP and ADP using functionalised gold nanoparticles. Org Biomol Chem 2018; 14:6811-20. [PMID: 27336846 DOI: 10.1039/c6ob00993j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diagnostic assays that incorporate a signal amplification mechanism permit the detection of analytes with enhanced selectivity. Herein, we report a gold nanoparticle-based chemical system able to differentiate ATP from ADP by means of catalytic signal amplification. The discrimination between ATP and ADP is of relevance for the development of universal assays for the detection of enzymes which consume ATP. For example, protein kinases are a class of enzymes critical for the regulation of cellular functions, and act to modulate the activity of other proteins by transphosphorylation, transferring a phosphate group from ATP to give ADP as a byproduct. The system described here exploits the ability of cooperative catalytic head groups on gold nanoparticles to very efficiently catalyze chromogenic reactions such as the transphosphorylation of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNPP). A series of chromogenic substrates have been synthesized and evaluated by means of Michaelis-Menten kinetics (compounds 2, 4-6). 2-Hydroxypropyl-(3-trifluoromethyl-4-nitro)phenyl phosphate (5) was found to display higher reactivity (kcat) and higher binding affinity (KM) when compared to HPNPP. This higher binding affinity allows phosphate 5 to compete with ATP and ADP to different extents for binding on the monolayer surface, thus enabling a catalytically amplified signal only when ATP is absent. Overall, this represents a viable new approach for monitoring the conversion of ATP into ADP with high sensitivity.
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Affiliation(s)
- Cristian Pezzato
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Jack L-Y Chen
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Patrizia Galzerano
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Michela Salvi
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
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24
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Sun X, Anslyn EV. An Auto‐Inductive Cascade for the Optical Sensing of Thiols in Aqueous Media: Application in the Detection of a VX Nerve Agent Mimic. Angew Chem Int Ed Engl 2017; 56:9522-9526. [DOI: 10.1002/anie.201704472] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Xiaolong Sun
- Department of Chemistry The University of Texas at Austin Austin TX 78712 USA
| | - Eric V. Anslyn
- Department of Chemistry The University of Texas at Austin Austin TX 78712 USA
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25
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Sun X, Anslyn EV. An Auto‐Inductive Cascade for the Optical Sensing of Thiols in Aqueous Media: Application in the Detection of a VX Nerve Agent Mimic. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Xiaolong Sun
- Department of Chemistry The University of Texas at Austin Austin TX 78712 USA
| | - Eric V. Anslyn
- Department of Chemistry The University of Texas at Austin Austin TX 78712 USA
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26
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Sun X, Dahlhauser SD, Anslyn EV. New Autoinductive Cascade for the Optical Sensing of Fluoride: Application in the Detection of Phosphoryl Fluoride Nerve Agents. J Am Chem Soc 2017; 139:4635-4638. [PMID: 28291353 DOI: 10.1021/jacs.7b01008] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new autoinductive cascade employing benzoyl fluoride as a latent source of fluoride is reported for signal amplification and optical detection of fluoride. The autoinduction leads to a maximum 4-fold signal enhancement for each fluoride generated, as well as a self-propagating cycle that generates three fluorophores for each single fluoride released. A two-step integrated protocol creates a more rapid autoinductive cascade than previously reported, as well as a highly sensitive diagnostic assay for the ultratrace quantitation of a phosphoryl fluoride nerve agent surrogate.
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Affiliation(s)
- Xiaolong Sun
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Samuel D Dahlhauser
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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27
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Gabrielli L, Mancin F. Minimal Self-Immolative Probe for Multimodal Fluoride Detection. J Org Chem 2016; 81:10715-10720. [DOI: 10.1021/acs.joc.6b01787] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Gabrielli
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35125 Padova, Italy
| | - Fabrizio Mancin
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35125 Padova, Italy
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28
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29
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Foli G, D'Elia CS, Fochi M, Bernardi L. Reversible modulation of the activity of thiourea catalysts with anions: a simple approach to switchable asymmetric catalysis. RSC Adv 2016. [DOI: 10.1039/c6ra12732k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A simple and straightforward approach to switchable asymmetric catalysis is presented, based on the interactions of thiourea catalysts with anions.
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Affiliation(s)
- Giacomo Foli
- Department of Industrial Chemistry “Toso Montanari” and INSTM RU Bologna
- Alma Mater Studiorum – University of Bologna
- 40136 Bologna
- Italy
| | - Cecilia Sasso D'Elia
- Department of Industrial Chemistry “Toso Montanari” and INSTM RU Bologna
- Alma Mater Studiorum – University of Bologna
- 40136 Bologna
- Italy
| | - Mariafrancesca Fochi
- Department of Industrial Chemistry “Toso Montanari” and INSTM RU Bologna
- Alma Mater Studiorum – University of Bologna
- 40136 Bologna
- Italy
| | - Luca Bernardi
- Department of Industrial Chemistry “Toso Montanari” and INSTM RU Bologna
- Alma Mater Studiorum – University of Bologna
- 40136 Bologna
- Italy
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30
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Vaquero M, Rovira L, Vidal-Ferran A. Supramolecularly fine-regulated enantioselective catalysts. Chem Commun (Camb) 2016; 52:11038-51. [DOI: 10.1039/c6cc04474c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of supramolecular interactions in catalysis has undergone major growth in the last decade and has contributed to the major advances achieved in the field of enantioselective catalysis.
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Affiliation(s)
- Mónica Vaquero
- Institute of Chemical Research of Catalonia (ICIQ) & The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
| | - Laura Rovira
- Institute of Chemical Research of Catalonia (ICIQ) & The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
| | - Anton Vidal-Ferran
- Institute of Chemical Research of Catalonia (ICIQ) & The Barcelona Institute of Science and Technology
- 43007 Tarragona
- Spain
- ICREA
- 08010 Barcelona
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31
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Chen S, Yamasaki M, Polen S, Gallucci J, Hadad CM, Badjić JD. Dual-Cavity Basket Promotes Encapsulation in Water in an Allosteric Fashion. J Am Chem Soc 2015; 137:12276-81. [PMID: 26348904 DOI: 10.1021/jacs.5b06041] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shigui Chen
- Department of Chemistry
and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Makoto Yamasaki
- Department of Chemistry
and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shane Polen
- Department of Chemistry
and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Judith Gallucci
- Department of Chemistry
and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Christopher M. Hadad
- Department of Chemistry
and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jovica D. Badjić
- Department of Chemistry
and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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32
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Liu G, Zhang G, Hu J, Wang X, Zhu M, Liu S. Hyperbranched Self-Immolative Polymers (hSIPs) for Programmed Payload Delivery and Ultrasensitive Detection. J Am Chem Soc 2015; 137:11645-55. [PMID: 26327337 DOI: 10.1021/jacs.5b05060] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Upon stimuli-triggered single cleavage of capping moieties at the focal point and chain terminal, self-immolative dendrimers (SIDs) and linear self-immolative polymers (l-SIPs) undergo spontaneous domino-like radial fragmentation and cascade head-to-tail depolymerization, respectively. The nature of response selectivity and signal amplification has rendered them a unique type of stimuli-responsive materials. Moreover, novel design principles are required for further advancement in the field of self-immolative polymers (SIPs). Herein, we report the facile fabrication of water-dispersible SIPs with a new chain topology, hyperbranched self-immolative polymers (hSIPs), by utilizing one-pot AB2 polycondensation methodology and sequential postfunctionalization. The modular engineering of three categories of branching scaffolds, three types of stimuli-cleavable capping moieties at the focal point, and seven different types of peripheral functional groups and polymeric building blocks affords both structurally and functionally diverse hSIPs with chemically tunable amplified-release features. On the basis of the hSIP platform, we explored myriad functions including visible light-triggered intracellular release of peripheral conjugated drugs in a targeted and spatiotemporally controlled fashion, intracellular delivery and cytoplasmic reductive milieu-triggered plasmid DNA release via on/off multivalency switching, mitochondria-targeted fluorescent sensing of H2O2 with a detection limit down to ∼20 nM, and colorimetric H2O2 assay via triggered dispersion of gold nanoparticle aggregates. To further demonstrate the potency and generality of the hSIP platform, we further configure it into biosensor design for the ultrasensitive detection of pathologically relevant antigens (e.g., human carcinoembryonic antigen) by integrating with enzyme-mediated cycle amplification with positive feedback and enzyme-linked immunosorbent assay (ELISA).
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Affiliation(s)
- Guhuan Liu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, iChem (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Guofeng Zhang
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, iChem (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China , Hefei, Anhui 230026, China.,Wuhan National Laboratory for Optoelectronics, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China
| | - Jinming Hu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, iChem (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Xiaorui Wang
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, iChem (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Mingqiang Zhu
- Wuhan National Laboratory for Optoelectronics, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China
| | - Shiyong Liu
- CAS Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, iChem (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China , Hefei, Anhui 230026, China
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33
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Singh AS, Sun SS. Structurally Flexible C₃-Symmetric Receptors for Molecular Recognition and Their Self-Assembly Properties. CHEM REC 2015. [PMID: 26202256 DOI: 10.1002/tcr.201500021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The bioinspired design and synthesis of building blocks and their assemblies by the supramolecular approach has ever fascinated scientists to utilize such artificial systems for numerous purposes. Flexibility is a basic feature of natural systems. However, in artificial systems this is difficult to control, especially if there is no preorganization of the component(s) of a system. We have designed and synthesized a series of C3 -symmetric N-bridged flexible receptors and successfully utilized them to selectively entrap the notorious and toxic nitrate anion in aqueous medium. This was the first report of highest binding affinity for the nitrate anion in aqueous medium. An impressive self-sorting phenomenon of reversibly formed hydrogen-bonded capsules, which self-assembled from flexible tripodal receptors having branches of similar size and bearing the same amide functionality, has been disclosed. Encapsulated nitrate anion has been further utilized for the photochemical [2+2] cycloaddition reaction for the synthesis of strained four-membered ring structures through dynamic self-assembly. In this Personal Account, we summarize these results showing the utility of naturally inspired flexibility in artificial systems.
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Affiliation(s)
- Ashutosh S Singh
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Institute of Physics Campus, Sachivalaya Marg, Near Sainik School, Bhubaneswar, 751005, India
| | - Shih-Sheng Sun
- Institute of Chemistry, Academia Sinica, 115 Nankang, Taipei, Taiwan.
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34
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Goggins S, Marsh BJ, Lubben AT, Frost CG. Signal transduction and amplification through enzyme-triggered ligand release and accelerated catalysis. Chem Sci 2015; 6:4978-4985. [PMID: 29142726 PMCID: PMC5664363 DOI: 10.1039/c5sc01588j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/13/2015] [Indexed: 01/20/2023] Open
Abstract
An enzyme-triggered catalytic signal amplification cascade is described through the design of a novel enzyme substrate that selectively activates an organometallic transfer hydrogenation catalyst once triggered.
Signal transduction and signal amplification are both important mechanisms used within biological signalling pathways. Inspired by this process, we have developed a signal amplification methodology that utilises the selectivity and high activity of enzymes in combination with the robustness and generality of an organometallic catalyst, achieving a hybrid biological and synthetic catalyst cascade. A proligand enzyme substrate was designed to selectively self-immolate in the presence of the enzyme to release a ligand that can bind to a metal pre-catalyst and accelerate the rate of a transfer hydrogenation reaction. Enzyme-triggered catalytic signal amplification was then applied to a range of catalyst substrates demonstrating that signal amplification and signal transduction can both be achieved through this methodology.
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Affiliation(s)
- Sean Goggins
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK . ; ; Tel: +44 (0)1225 386142
| | - Barrie J Marsh
- Atlas Genetics , Derby Court, Epsom Square, White Horse Business Park, Trowbridge , Wiltshire , BA14 0XG , UK . ; Tel: +44 (0)1225 717932
| | - Anneke T Lubben
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK . ; ; Tel: +44 (0)1225 386142
| | - Christopher G Frost
- Department of Chemistry , University of Bath , Bath , BA2 7AY , UK . ; ; Tel: +44 (0)1225 386142
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35
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Selvakumar K, Motiei L, Margulies D. Enzyme-Artificial Enzyme Interactions as a Means for Discriminating among Structurally Similar Isozymes. J Am Chem Soc 2015; 137:4892-5. [PMID: 25819325 DOI: 10.1021/jacs.5b02496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We describe the design and function of an artificial enzyme-linked receptor (ELR) that can bind different members of the glutathione-S-transferase (GST) enzyme family. The artificial enzyme-enzyme interactions distinctly affect the catalytic activity of the natural enzymes, the biomimetic, or both, enabling the system to discriminate among structurally similar GST isozymes.
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Affiliation(s)
| | - Leila Motiei
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel 76100
| | - David Margulies
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel 76100
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36
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Wang CW, Yu WT, Lai HP, Lee BY, Gao RC, Tan KT. Steric-dependent label-free and washing-free enzyme amplified protein detection with dual-functional synthetic probes. Anal Chem 2015; 87:4231-6. [PMID: 25811916 DOI: 10.1021/ac504398g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Enzyme-catalyzed signal amplification with an antibody-enzyme conjugate is commonly employed in many bioanalytical methods to increase assay sensitivity. However, covalent labeling of the enzyme to the antibody, laborious operating procedures, and extensive washing steps are necessary for protein recognition and signal amplification. Herein, we describe a novel label-free and washing-free enzyme-amplified protein detection method by using dual-functional synthetic molecules to impose steric effects upon protein binding. In our approach, protein recognition and signal amplification are modulated by a simple dual-functional synthetic probe which consists of a protein ligand and an inhibitor. In the absence of the target protein, the inhibitor from the dual-functional probe would inhibit the enzyme activity. In contrast, binding of the target protein to the ligand perturbs this enzyme-inhibitor affinity due to the generation of steric effects caused by the close proximity between the target protein and the enzyme, thereby activating the enzyme to initiate signal amplification. With this strategy, the fluorescence signal can be amplified to as high as 70-fold. The generality and versatility of this strategy are demonstrated by the rapid, selective, and sensitive detection of four different proteins, avidin, O6-methylguanine DNA methyltransferase (MGMT), SNAP-tag, and lactoferrin, with four different probes.
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Affiliation(s)
- Chia-Wen Wang
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Wan-Ting Yu
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Hsiu-Ping Lai
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Bing-Yuan Lee
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Ruo-Cing Gao
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
| | - Kui-Thong Tan
- †Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC).,‡Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd., Hsinchu 30013, Taiwan (ROC)
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37
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Miao P, Tang Y, Wang B, Yin J, Ning L. Signal amplification by enzymatic tools for nucleic acids. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.12.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Rationally designing aptamer sequences with reduced affinity for controlled sensor performance. SENSORS 2015; 15:7754-67. [PMID: 25835184 PMCID: PMC4431182 DOI: 10.3390/s150407754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 12/30/2022]
Abstract
The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7–18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes.
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39
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Yoshii T, Onogi S, Shigemitsu H, Hamachi I. Chemically Reactive Supramolecular Hydrogel Coupled with a Signal Amplification System for Enhanced Analyte Sensitivity. J Am Chem Soc 2015; 137:3360-5. [DOI: 10.1021/ja5131534] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tatsuyuki Yoshii
- Department
of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Shoji Onogi
- Department
of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Hajime Shigemitsu
- Department
of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
- Japan Science and Technology Agency (JST), CREST, Gobancho, Chiyoda-ku, Tokyo 102-0075, Japan
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40
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Foy JT, Ray D, Aprahamian I. Regulating signal enhancement with coordination-coupled deprotonation of a hydrazone switch. Chem Sci 2015; 6:209-213. [PMID: 28553470 PMCID: PMC5433045 DOI: 10.1039/c4sc02882a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 01/27/2023] Open
Abstract
Proton relay plays an important role in many biocatalytic pathways. In order to mimic such processes in the context of molecular switches, we developed coordination-coupled deprotonation (CCD) driven signaling and signal enhancement sequences. This was accomplished by using the zinc(ii)-initiated CCD of a hydrazone switch to instigate an acid catalyzed imine bond hydrolysis that separates a quencher from a fluorophore thus leading to emission amplification. Because CCD is a reversible process, we were able to show that the catalysis can be regulated and turned "on" and "off" using a metalation/demetalation cycle.
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Affiliation(s)
- Justin T Foy
- SAMS Research Group , University of Strasbourg , Institut Charles Sadron , CNRS , 23 rue du Loess, BP84047 , 67034 , Strasbourg Cedex 2 , France
| | - Debdas Ray
- Department of Chemistry , School of Natural Sciences , Shiv Nadar University , Chithera, Tehsil Dadri , Gautam Budh Nagar-203207 , Uttar Pradesh , India
| | - Ivan Aprahamian
- Department of Chemistry , Dartmouth College , 6128 Burke Laboratory , Hanover , NH , USA 03755 .
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41
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Jiaul Haque AM, Kim J, Dutta G, Kim S, Yang H. Redox cycling-amplified enzymatic Ag deposition and its application in the highly sensitive detection of creatine kinase-MB. Chem Commun (Camb) 2015; 51:14493-6. [DOI: 10.1039/c5cc06117b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This communication reports a novel enzymatic Ag-deposition scheme combined with chemical–chemical redox cycling by reduced β-nicotinamide adenine dinucleotide.
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Affiliation(s)
- Al-Monsur Jiaul Haque
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
| | - Jihye Kim
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
| | - Gorachand Dutta
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine
- Yonsei University College of Medicine
- Seoul 135-720
- Korea
| | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
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42
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Gu JA, Mani V, Huang ST. Design and synthesis of ultrasensitive off–on fluoride detecting fluorescence probe via autoinductive signal amplification. Analyst 2015; 140:346-52. [DOI: 10.1039/c4an01723d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Design and synthesis of an ultrasensitive fluorescence probeviaautoinductive signal amplification for picomolar detection of fluoride.
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Affiliation(s)
- Jiun-An Gu
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei
- Republic of China
| | - Veerappan Mani
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei
- Republic of China
| | - Sheng-Tung Huang
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei
- Republic of China
- Graduate Institute of Biomedical and Biochemical Engineering
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43
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Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. J Am Chem Soc 2014; 136:17692-701. [PMID: 25474128 PMCID: PMC4291754 DOI: 10.1021/ja510028c] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 02/07/2023]
Abstract
Linking cell signaling events to the fundamental physicochemical basis of the conformational behavior of single molecules and ultimately to cellular function is a key challenge facing the life sciences. Here we outline the emerging principles of allosteric interactions in cell signaling, with emphasis on the following points. (1) Allosteric efficacy is not a function of the chemical composition of the allosteric pocket but reflects the extent of the population shift between the inactive and active states. That is, the allosteric effect is determined by the extent of preferred binding, not by the overall binding affinity. (2) Coupling between the allosteric and active sites does not decide the allosteric effect; however, it does define the propagation pathways, the allosteric binding sites, and key on-path residues. (3) Atoms of allosteric effectors can act as "driver" or "anchor" and create attractive "pulling" or repulsive "pushing" interactions. Deciphering, quantifying, and integrating the multiple co-occurring events present daunting challenges to our scientific community.
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Affiliation(s)
- Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler
Institute of Molecular Medicine, Department of Human Genetics and
Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jin Liu
- Department
of Biophysics, University of Texas Southwestern
Medical Center, 5323
Harry Hines Boulevard, Dallas, Texas 75390, United
States
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
and Center for Scientific Computation, Southern
Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275, United
States
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44
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Bardelang D, Casano G, Poulhès F, Karoui H, Filippini J, Rockenbauer A, Rosas R, Monnier V, Siri D, Gaudel-Siri A, Ouari O, Tordo P. Spin Exchange Monitoring of the Strong Positive Homotropic Allosteric Binding of a Tetraradical by a Synthetic Receptor in Water. J Am Chem Soc 2014; 136:17570-7. [DOI: 10.1021/ja509586k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- David Bardelang
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Gilles Casano
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Florent Poulhès
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Hakim Karoui
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Jessica Filippini
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Antal Rockenbauer
- Department of Physics, Budapest University of Technology and Economics and MTA-BME Condensed Matter Research Group, Budafoki ut 8, 1111 Budapest, Hungary
| | - Roselyne Rosas
- Aix-Marseille Université, CNRS, Spectropole, FR 1739, 13013 Marseille, France
| | - Valérie Monnier
- Aix-Marseille Université, CNRS, Spectropole, FR 1739, 13013 Marseille, France
| | - Didier Siri
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Anouk Gaudel-Siri
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
| | - Paul Tordo
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, UMR 7273, 13397 Marseille, France
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45
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Li J, Nowak P, Otto S. An Allosteric Receptor by Simultaneous “Casting” and “Molding” in a Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Li J, Nowak P, Otto S. An allosteric receptor by simultaneous "casting" and "molding" in a dynamic combinatorial library. Angew Chem Int Ed Engl 2014; 54:833-7. [PMID: 25430978 DOI: 10.1002/anie.201408907] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/31/2014] [Indexed: 01/13/2023]
Abstract
Allosteric synthetic receptors are difficult to access by design. Herein we report a dynamic combinatorial strategy towards such systems based on the simultaneous use of two different templates. Through a process of simultaneous casting (the assembly of a library member around a template) and molding (the assembly of a library member inside the binding pocket of a template), a Russian-doll-like termolecular complex was obtained with remarkable selectivity. Analysis of the stepwise formation of the complex indicates that binding of the two partners by the central macrocycle exhibits significant positive cooperativity. Such allosteric systems represent hubs that may have considerable potential in systems chemistry.
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Affiliation(s)
- Jianwei Li
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.otto-lab.com
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47
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Plaunt AJ, Clear KJ, Smith BD. ¹⁹F NMR indicator displacement assay using a synthetic receptor with appended paramagnetic relaxation agent. Chem Commun (Camb) 2014; 50:10499-501. [PMID: 25069015 PMCID: PMC4162400 DOI: 10.1039/c4cc04159c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An admixture of zinc(II)-bis(dipicolylamine) receptor with covalently attached paramagnetic relaxation agent and fluorine-labeled phosphate indicator enables (19)F NMR detection of phosphorylated analytes with amplified switched-on signal intensity.
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Affiliation(s)
- Adam J Plaunt
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, IN, USA.
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48
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Fanlo-Virgós H, Alba ANR, Hamieh S, Colomb-Delsuc M, Otto S. Transient substrate-induced catalyst formation in a dynamic molecular network. Angew Chem Int Ed Engl 2014; 53:11346-50. [PMID: 25169198 DOI: 10.1002/anie.201403480] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/02/2014] [Indexed: 11/06/2022]
Abstract
In biology enzyme concentrations are continuously regulated, yet for synthetic catalytic systems such regulatory mechanisms are underdeveloped. We now report how a substrate of a chemical reaction induces the formation of its own catalyst from a dynamic molecular network. After complete conversion of the substrate, the network disassembles the catalyst. These results open up new opportunities for controlling catalysis in synthetic chemical systems.
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Affiliation(s)
- Hugo Fanlo-Virgós
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.otto-lab.com
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49
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Fanlo-Virgós H, Alba ANR, Hamieh S, Colomb-Delsuc M, Otto S. Transient Substrate-Induced Catalyst Formation in a Dynamic Molecular Network. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403480] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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50
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Kremer C, Lützen A. Allosteric binding of capsaicin by a bis(β-cyclodextrin)-2,2'-bipyridine receptor. Chemistry 2014; 20:8852-5. [PMID: 24953045 DOI: 10.1002/chem.201403503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 11/07/2022]
Abstract
A new β-cyclodextrin-based receptor that showed allosteric binding behavior towards capsaicin in aqueous solution was prepared. By NMR titration and nonlinear regression, we obtained binding constants, which increased more than fivefold when an effector (Zn(2+)) was bound to a central 2,2'-bipyridine that acts as the allosteric center.
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Affiliation(s)
- Christopher Kremer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany), Fax: (+49) 228-73-9608
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